BLASTP 2.2.26 [Sep-21-2011]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= 026329
         (240 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|3EH1|A Chain A, Crystal Structure Of The Human Copii-Coat Protein Sec24b
          Length = 751

 Score = 28.1 bits (61), Expect = 4.0,   Method: Composition-based stats.
 Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 8/42 (19%)

Query: 14  ISLTDRPKWQQFLICSSGFFFGYLVNGVCEEYVYNRLQFSYG 55
           +S  D+ +W+    C+      Y VN V EE++YN L  SYG
Sbjct: 99  VSFIDQRRWK----CN----LCYRVNDVPEEFMYNPLTRSYG 132


>pdb|4F3S|A Chain A, Crystal Structure Of Periplasmic D-Alanine Abc Transporter
           From Salmonella Enterica
          Length = 255

 Score = 27.3 bits (59), Expect = 8.7,   Method: Compositional matrix adjust.
 Identities = 29/118 (24%), Positives = 50/118 (42%), Gaps = 12/118 (10%)

Query: 13  GISLTDRPKWQQFLICSSGFFFG--YLVNGVCEEYVYNRLQFSYGWYFTFIQGFVYLVLI 70
           GIS+TD+ K  + +  S  ++    YLV+    +   N L     +   + +G  Y  LI
Sbjct: 75  GISITDKRK--KVIDFSEPYYINSFYLVSXANHKITLNNLNELNKYSIGYPRGXAYSDLI 132

Query: 71  Y----LQGFTTKQMMNPWKTYVKLSAVLMGSHGLTKGSLAFLNYPAQLMFKSTKVLPV 124
                 +G+ +   +  + TY +  A L   +      LAF+  P    FK+ K  P+
Sbjct: 133 KNDLEPKGYYSLSKVKLYPTYNETXADLKNGNL----DLAFIEEPVYFTFKNKKKXPI 186


>pdb|4DZ1|A Chain A, Crystal Structure Of Dals, An Atp Binding Cassette
           Transporter For D- Alanine From Salmonella Enterica
          Length = 259

 Score = 26.9 bits (58), Expect = 9.9,   Method: Compositional matrix adjust.
 Identities = 29/118 (24%), Positives = 50/118 (42%), Gaps = 12/118 (10%)

Query: 13  GISLTDRPKWQQFLICSSGFFFG--YLVNGVCEEYVYNRLQFSYGWYFTFIQGFVYLVLI 70
           GIS+TD+ K  + +  S  ++    YLV+    +   N L     +   + +G  Y  LI
Sbjct: 95  GISITDKRK--KVIDFSEPYYINSFYLVSXANHKITLNNLNELNKYSIGYPRGXAYSDLI 152

Query: 71  YL----QGFTTKQMMNPWKTYVKLSAVLMGSHGLTKGSLAFLNYPAQLMFKSTKVLPV 124
                 +G+ +   +  + TY +  A L   +      LAF+  P    FK+ K  P+
Sbjct: 153 KNDLEPKGYYSLSKVKLYPTYNETXADLKNGNL----DLAFIEEPVYFTFKNKKKXPI 206


  Database: pdbaa
    Posted date:  Mar 3, 2013 10:34 PM
  Number of letters in database: 14,973,337
  Number of sequences in database:  62,578
  
Lambda     K      H
   0.327    0.139    0.433 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,151,733
Number of Sequences: 62578
Number of extensions: 210313
Number of successful extensions: 481
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 481
Number of HSP's gapped (non-prelim): 4
length of query: 240
length of database: 14,973,337
effective HSP length: 96
effective length of query: 144
effective length of database: 8,965,849
effective search space: 1291082256
effective search space used: 1291082256
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 50 (23.9 bits)